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Structural flexibility of regulatory DNA element
Řezáčová, Barbora ; Štěpánek, Josef (advisor) ; Rosenberg, Ivan (referee)
Transcription of the genetic code is controlled by numerous proteins. Some of them, so-called transcription factors, bind to certain DNA regions possessing anomalous properties due to their specific and highly conservative base sequence. One of these DNA segments is SRE (Serum Response Element). The diploma work is linked to results of the previous study indicating that the structural flexibility of this segment, related to the CArG box sequence, plays a key role in its physiological activity. Our work is devoted to study of this DNA segment and its model sequential variants. The approach of accurate measurements of temperature dependent UV absorption spectra and their consecutive analysis by means of factor analysis techniques and difference spectra construction, the main part of which was also developed within the framework of this work, was employed. The results indicate that separate chains of SRE with various length form surprisingly stable hairpins, which in some cases prevail even in mixtures of both chains of the SRE segment over duplexes. By using a fitting to thermodynamic equilibrium equations, thermodynamic characteristics of temperature induced association and dissociation transitions of complexes, both intermolecular (duplexes) and intramolecular (hairpins), were obtained.
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Synthesis of Prolinol-Based Phosphonate Nucleotide Analogues
Vaněk, Václav ; Rosenberg, Ivan (advisor) ; Černý, Miloslav (referee) ; Moravcová, Jitka (referee) ; Pour, Milan (referee)
4. Conclusion A series ofnovel isosteric 3'-nucleotide analogues (9a-e and l0a-e) was synthesized, cr-t-- and B-t--prolinol nucleoside N-methylphosphonic acids distinguished for the loss of unambiguously defined configuration at the nitrogen atom in 3'-position of prolinol nng. Remarkable conformational differences between cr-L- and B-l-prolinol nucleotides determined by NMR study suggest some similarity with the natural 5'-o-nucleotide. The same conformational changes in o-series of prolinol nucleotides fit even better the 3'- and 5'-o- nucleotides. In addition, a series of four diastereoisomeric synthons 5-8 was prepared from the commercially available lrans-4-hydroxy-l-proline, giving access to a complete set of prolinol-derived nucleotide analogues bearing cr.L-, B-t--, o.o- and p-o-conÍiguration. In order to constrain the conformational flexibility of the N-phosphonomethyl moiety, seveÍal protected compounds were subjected to N-oxidation or N-methylation which gave chiral N-oxides or quatemary ammonium salts. However, the synthesis of the respective unprotected phosphonic acids was unsuccessful, probably due to their fast decomposition. Acylation ofthe pyrrolidine ring nitrogen atom by several acylphosphonic acid derivatives led to the novel N.phosphonoformyl, /y'.phosphonoacetyl and...
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Synthesis, reactivity and biological activity of C5 substituted uracil analogues
Brulíková, Lucie ; Holý, Antonín (advisor) ; Rosenberg, Ivan (referee) ; Moravcová, Jitka (referee)
Bibliographical identification: Author's first name and surname: RNDr. Lucie Brulíková (nee Spáčilová) Title: Synthesis, reactivity and biological activity of C-5 substituted uracil analogues Type of thesis: Ph.D. thesis Department: Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc Advisor: prof. RNDr. Antonín Holý, Dr.Sc., Dr.hc. mult. Advisor-consultant: doc. RNDr. Jan Hlaváč, Ph.D. The year of presentation: 2011 Abstract: The presented thesis is focused on the synthesis of various C-5 modified uracil analogues, the study of their reactivity and biological activity, especially cytotoxic activity. In the first part, the brief survey of described results for selected 5-alkoxymethyluracil analogues is performed. The second part of the presented thesis deals with the synthesis of novel uracil analogues modified at the C-5 position, the development and optimizing of procedure leading to the desired compounds, the study of biological activity and the evaluation of structure- activity relationship (SAR). This part presents the synthesis of a series of 5-[alkoxy(4- nitrophenyl)methyl)]uracil and 5-alkoxymethyluracil analogues and extended SAR studies depending on a substitution of metylene bridge directly attached at the C-5 position as well as alkoxy chain length. The last part of...
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Synthesis of ellipticine derivatives and study of their interactions with DNA
Dračínský, Martin ; Sejbal, Jan (advisor) ; Klinot, Jiří (referee) ; Lyčka, Antonín (referee) ; Rosenberg, Ivan (referee)
CONCLUSIONS t New strategy for ellipticine synthesis was proposed' The yields of the synthesis are very hígh and pure product is obtained. The strategy was verified with the synthesis of other ellipticine derivatives' rBenzylicoxidationsoťellipticineandl,4-dimethylcarbazolewerestudiedand13. hydroxyellipticine was slnthesised' ' Three empirical potentials were compared with reference ab initio data of ellipticine derivative - DNA base patr' . The ernpirical potentials calculate interaction energies of the complexes quite well (espeglallytheA-ffE6andtheLHpotentials)buttheyfailinthesearchofglobal energy minima geometri es' .Interactionsofellipticineandg.hydroxyellipticinewithtwooligonucleotideswerc studiedintwobuffers(weaklyacidicandneutral,ellipticineisprotonatedintlro acidic buffer). Using two-dimensional NMR techniques assignment of all hydrogen signals of oligonucleotides CGCTAGCG and ATAGCTAT was done. The most important interaction of the ellipticine derivatives with the oligonucleotides is intercalation, but in the acidic buffer ellipticine can form also non-intercalative (bond to the minor or to the major groove) complexes with the oligonucleotides. Both ellipticine derivatives destabilised the duplex structuÍe of the oligonucleotide ATAGCTAT in acidic environment. ln the neutral buffer the life-time...
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Synthesis of nucleosides, nucleotides and nucleic acids bearing bipyridine-type ligands
Kalachová, Ľubica ; Hocek, Michal (advisor) ; Stiborová, Marie (referee) ; Rosenberg, Ivan (referee)
An efficient methodology of construction of base-modified nucleosides bearing oligopyridine ligands, based on the Sonogashira or Suzuki cross-coupling reaction of halogenated nucleosides, was developed. This methodology was then successfully employed in construction of base-modified DNA bearing oligopyridine ligands which were studied in post-synthetic complexation with labile transition metals. The first step in construction of modified DNA is the synthesis of deoxynucleoside triphosphate (dNTPs) bearing various metal chelating groups, which are in second step enzymatically incorporated into DNA by primer extension experiment. The first task was the synthesis of dNTPs bearing different oligopyridine ligands, which could be done by aqueous phase cross-coupling reaction with suitable building blocks or by triphosphorylation of oligopyridine-modified deoxynucleosides. Both ways were successfully used. Aqueous phase Sonogashira cross-coupling was used for synthesis of dNTPs bearing oligopyridine ligands attached via short and rigid acetylene tether, while classical triphosphorylation of modified nucleosides was used for construction of dNTPs bearing oligopyridine ligands attached via long and flexible octadiyne linker. Sonogashira cross-coupling reaction was also used for preparation of both types of...
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Synthesis of purine and pyrimidine derivatives with potential biological activities.
Jansa, Petr ; Holý, Antonín (advisor) ; Černý, Miloslav (referee) ; Rosenberg, Ivan (referee)
An extensive overview of the current state of the research in the field of the development of acyclic nucleoside phosphonates (ANPs) was elaborated, which quotes from 196 publications in abstracted journals. A new microwave-assisted methodology for the preparation of dialkyl haloalkylphosphonates was developed. Through strict control of the reaction temperatures in microwave reactor, it was possible to lower the amount of the reactants all the way to the ideal ratio of 1:1. With the use of a continuous-flow microwave reactor, it was possible to prepare the key building blocks for the subsequent syntheses of ANPs in large quantities (100 g), which significantly accelerates research in this area. The new method was patented and published. While studying various ANP prodrugs, a new highly effective methodology for the preparation of the diamides of ANPs was developed. The method starts directly from ANP diesters, which react with trimethylsilylbromide to form the corresponding bis(trimethylsilyl)esters of ANPs, which are well soluble in organic solvents and react smoothly during the subsequent introduction of aminoacid esters. Moreover, the reaction with trimethylsilylbromide protects the reactive groups present in the rest of the molecule and thus prevents undesired side reactions. Furthermore, using...
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Synthesis, reactivity and biological activity of C5 substituted uracil analogues
Brulíková, Lucie ; Holý, Antonín (advisor) ; Rosenberg, Ivan (referee) ; Moravcová, Jitka (referee)
Bibliographical identification: Author's first name and surname: RNDr. Lucie Brulíková (nee Spáčilová) Title: Synthesis, reactivity and biological activity of C-5 substituted uracil analogues Type of thesis: Ph.D. thesis Department: Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc Advisor: prof. RNDr. Antonín Holý, Dr.Sc., Dr.hc. mult. Advisor-consultant: doc. RNDr. Jan Hlaváč, Ph.D. The year of presentation: 2011 Abstract: The presented thesis is focused on the synthesis of various C-5 modified uracil analogues, the study of their reactivity and biological activity, especially cytotoxic activity. In the first part, the brief survey of described results for selected 5-alkoxymethyluracil analogues is performed. The second part of the presented thesis deals with the synthesis of novel uracil analogues modified at the C-5 position, the development and optimizing of procedure leading to the desired compounds, the study of biological activity and the evaluation of structure- activity relationship (SAR). This part presents the synthesis of a series of 5-[alkoxy(4- nitrophenyl)methyl)]uracil and 5-alkoxymethyluracil analogues and extended SAR studies depending on a substitution of metylene bridge directly attached at the C-5 position as well as alkoxy chain length. The last part of...
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